Team:KULeuven/Modeling/Blue Light Receptor

From 2009.igem.org

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{{Team:KULeuven/Common2/EndHeader}}
{{Team:KULeuven/Common2/EndHeader}}
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=Blue light Sensor=
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__NOTOC__
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=Blue Light Receptor: Modeling=
==Biological Model==
==Biological Model==
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[[image:Bls.JPG|650px|center]]
[[image:Bls.JPG|650px|center]]
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==Simulation=
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<center>
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{| width=80% style="border: 1px solid #003E81; background-color: #EEFFFF;"
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|+ ''Parameter values (Vanillin Sensor)''
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! width=15% | Name
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! width=15% | Value
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! width=40% | Comments
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! width=10% | Reference
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|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation Rates
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|-
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| d<sub>mRNA</sub>
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| 2.3105E-3 s<sup>-1</sup>
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|
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [3<html>]</html>]
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|-
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| d<sub>Proteins</sub>
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| 1.9254E-5 s<sup>-1</sup>
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|
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [4<html>]</html>]
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|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates
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|-
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| k<sub>YcgF</sub>
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| 0.0154 s<sup>-1</sup>
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| Rate is faster than transcription rate of YcgE
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [1<html>]</html>]
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|-
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| k<sub>YcgE</sub>
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| 0.00848 s<sup>-1</sup>
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| estimate
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [1<html>]</html>]
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|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates
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|-
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| k<sub>YcgF</sub>
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| 0.167s<sup>-1</sup>
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| Rate is faster than transcription rate of YcgE
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [5<html>]</html>]
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|-
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| k<sub>YcgE</sub>
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| 0.167 s<sup>-1</sup>
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| estimate
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [5<html>]</html>]
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|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Dimerization Parameters
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|-
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| k<sub>dimerization</sub>
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| 8.0E-11 (s W/m^2)<sup>-1</sup>
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| Rate of dimerization of YcgF
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [1<html>]</html>]
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|-
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| k<sub>dissociation</sub>
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| 0.0058 s<sup>-1</sup>
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| Rate of dissociation of the YcgF complex
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [2<html>]</html>]
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|-
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! colspan="4" style="border-bottom: 1px solid #003E81;" | YcgF/YcgE Interaction
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|-
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| k<sub>bind</sub>
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| 100 (s molecule)<sup>-1</sup>
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| Rate of binding of YcgF dimer to YcgE
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [1<html>]</html>]
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|-
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| k<sub>unbind</sub>
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| 1 s<sup>-1</sup>
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| Rate of dissociation of the YcgF/YcgE complex
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| [https://2009.igem.org/Team:KULeuven/Modelling/Vanillin_Production#References [1<html>]</html>]
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|-
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|}
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</center>
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==Simulation==
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The amount of produced RIBOKEY is positively correlated on the incident blue radiation. The build up of key in the begin period of is due to the relative slow build up of the active state of YcgF protein in compared to the build up of YcgE.
[[image:Blue_light_sensor.png|700px|center]]
[[image:Blue_light_sensor.png|700px|center]]
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[2] Y. Nakasone et al., "Transient Dimerization and Conformational Change of a BLUF Protein:  YcgF", Journal of the American Chemical Society, Apr. 2006
[2] Y. Nakasone et al., "Transient Dimerization and Conformational Change of a BLUF Protein:  YcgF", Journal of the American Chemical Society, Apr. 2006
 +
 +
[3] J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, Jul. 2002, pp. 9697–9702
 +
 +
[4] K. Nath et al., “Protein degradation in Escherichia Coli,” The Journal of Biological Chemistry, vol. 246, Nov. 1971, pp. 6956-6967
 +
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[5] S.L. Gotta et al., “rRNA Transcription Rate in Escherichia Coli,” Journal of Bacteriology, vol. 173, Oct. 1991, pp. 6647-6649
 +
{{Team:KULeuven/Common2/PageFooter}}
{{Team:KULeuven/Common2/PageFooter}}

Latest revision as of 12:49, 18 October 2009


Blue Light Receptor: Modeling

Biological Model

Biologie blue light.png

Mathematical Model

Bls.JPG
Parameter values (Vanillin Sensor)
Name Value Comments Reference
Degradation Rates
dmRNA 2.3105E-3 s-1 [3]
dProteins 1.9254E-5 s-1 [4]
Transcription Rates
kYcgF 0.0154 s-1 Rate is faster than transcription rate of YcgE [1]
kYcgE 0.00848 s-1 estimate [1]
Translation Rates
kYcgF 0.167s-1 Rate is faster than transcription rate of YcgE [5]
kYcgE 0.167 s-1 estimate [5]
Dimerization Parameters
kdimerization 8.0E-11 (s W/m^2)-1 Rate of dimerization of YcgF [1]
kdissociation 0.0058 s-1 Rate of dissociation of the YcgF complex [2]
YcgF/YcgE Interaction
kbind 100 (s molecule)-1 Rate of binding of YcgF dimer to YcgE [1]
kunbind 1 s-1 Rate of dissociation of the YcgF/YcgE complex [1]

Simulation

The amount of produced RIBOKEY is positively correlated on the incident blue radiation. The build up of key in the begin period of is due to the relative slow build up of the active state of YcgF protein in compared to the build up of YcgE.

Blue light sensor.png

References

[1] Natalia Tschowri, Susan Busse and Regine Hengge, "The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli"

[2] Y. Nakasone et al., "Transient Dimerization and Conformational Change of a BLUF Protein: YcgF", Journal of the American Chemical Society, Apr. 2006

[3] J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, Jul. 2002, pp. 9697–9702

[4] K. Nath et al., “Protein degradation in Escherichia Coli,” The Journal of Biological Chemistry, vol. 246, Nov. 1971, pp. 6956-6967

[5] S.L. Gotta et al., “rRNA Transcription Rate in Escherichia Coli,” Journal of Bacteriology, vol. 173, Oct. 1991, pp. 6647-6649

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